iiinova — where your digital self keeps evolving

Shujun Ou @sigmafacto.bsky.social · 12/08/2026

Tenure-track Assistant Professor position available in my department at Ohio State. People using imaging, quantitative biology, computational biology, multi-omics or systems biology in any area of Eukaryotic Developmental Biology, Cell Biology, or Genomics are welcome to apply!

osu.wd1.myworkdayjobs.com

Assistant Professor of Molecular Genetics

Screen reader users may encounter difficulty with this site. For assistance with applying, please contact hr-accessibleapplication@osu.edu. If you have questions while submitting an application, pleas...

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Shujun Ou @sigmafacto.bsky.social · 27/07/2026

We reengineered the TIR-Learner for 60-100 times faster de novo search of Terminal Inverted Repeat transposons. We completed annotating 579 vertebrate genomes in 4 hours! Kenji Gerhardt did all the heavy lifting for this "side project".

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Shujun Ou @sigmafacto.bsky.social · 09/07/2026

Thank you for your early contributions!!!

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Reposted by Shujun Ou

John Fowler (he/him) @jefowlerjr.bsky.social · 13/05/2026

Interesting new preprint from the Ou lab, using long-read sequencing to characterize transcriptional initiation in LTR transposons in maize

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Shujun Ou @sigmafacto.bsky.social · 19/03/2026

I improved non-LTR detection by developing the AnnoSINEv2 and adding RepeatModeler2 to EDTA. It was updated a while ago (since v2.2 I believe). Please check out our latest v2.3, which supports full-length LTR-RT in the library: github.com/oushujun/EDT.... We also applied EDTA2 on >500 vertebrates.

github.com

Releases · oushujun/EDTA

Extensive de-novo TE Annotator . Contribute to oushujun/EDTA development by creating an account on GitHub.

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Shujun Ou @sigmafacto.bsky.social · 27/07/2025

Summer Grill Heave Of Ou Lab (SGHOOL) and families!

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Shujun Ou @sigmafacto.bsky.social · 09/06/2025

The position is filled. Thank you all for helping to spread the word!

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Shujun Ou @sigmafacto.bsky.social · 07/06/2025

TESS is an open-source package developed by Dr. Chris Benson (Ohio State), Dr. Ting-Hsuan Chen (NZ Plant & Food) & Mr. Tianyu Lu (Ohio State Senior UG). The study is conceived with Drs. Susan Thomson and Cecilia Deng (NZ Plant & Food). Please try it out! /n github.com/cwb14/TESS/t...

github.com

GitHub - cwb14/TESS: A Forward Simulation Framework for Studying the Role of Transposable Elements in Genome Expansion and Contraction

A Forward Simulation Framework for Studying the Role of Transposable Elements in Genome Expansion and Contraction - cwb14/TESS

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Shujun Ou @sigmafacto.bsky.social · 07/06/2025

Using TESS and parameter sweep, we were able to approximate the TE dynamics of these three rust fungus genomes, revealing the two-stage evolution of myrtle rust (A. psidii), with a long-lasting genome expansion transitioned to aggressive contraction ~1.2 million generations ago.

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Shujun Ou @sigmafacto.bsky.social · 07/06/2025

We selected three extreme cases, being fast insertion/fast deletion/stable genome (Cronartium ribicola), slow insertion/slow deletion/stable genome (Puccinia coronata), and fast insertion/slow deletion/obese genome (Austropuccinia psidii), typical of eukaryotic genome dynamics.

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Shujun Ou @sigmafacto.bsky.social · 07/06/2025

What can TESS achieve? We used it to study the genome evolution dynamics of Pucciniomycotina, a subdivision of rust fungi with 58 high-quality genomes available and sizes varying from 20 Mb to 1018 Mb, mostly due to TE dynamics!

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Shujun Ou @sigmafacto.bsky.social · 07/06/2025

The PrinTE component of TESS makes genomes live on silicon chips! It can simulate TE insertions and deletions at any rates and dynamics, including complete deletions or creation of solo LTRs, and allow genomes to evolve forward in time. Here is one simulation of a digital genome:

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Shujun Ou @sigmafacto.bsky.social · 07/06/2025

The third mode of TEgenomeSimulator can simulate genomes with almost identical size, TE content, TE length distribution, and a normalized TE divergence (for ease of modeling) to real genomes - essentially digital replicas. This powerful mode allows in-silico genome evolution!

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Shujun Ou @sigmafacto.bsky.social · 07/06/2025

The TEgenomeSimulator component has three modes, which can simulate genomes representing snapshots of TE evolution at different stages: ancient expansion, recent expansion, long-lasting burst, and short burst.

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Shujun Ou @sigmafacto.bsky.social · 07/06/2025

The RandSeqInsert component can simulate TIR transposon insertions using a live-updated, high-performance AVL tree structure. It takes user-provided TIR libraries and allows setting varying lengths of target site duplications and nested insertions that mimic true TE insertions.

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Shujun Ou @sigmafacto.bsky.social · 07/06/2025

I want to share our latest work on a forward simulation framework on transposable element evolution. The TE Evolution Simulation Suite, or TESS, contains three components that can simulate many scenarios of genome evolution under the impact of TEs.

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Shujun Ou @sigmafacto.bsky.social · 07/06/2025

At this point, we still need human experts to distinguish AI-generated papers from authentic manuscripts, and even this fails quite frequently. Without peer review as gatekeepers, manuscript posting may become somewhat like blogging. Non-specialists will have a hard time distinguishing make-ups.

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Shujun Ou @sigmafacto.bsky.social · 24/04/2025

I start to screen for interview candidates. If you are interested, please hurry up!

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Shujun Ou @sigmafacto.bsky.social · 10/04/2025

The job is at Ohio State University located in Columbus, Ohio, a very commutable, affordable, and livable city with enriched food, nature, and culture. We are a fun, diverse group that care for each other and promote individual success. Please help to repost! Thank you for your attention! 3/3

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Shujun Ou @sigmafacto.bsky.social · 10/04/2025

The position will need to drive the project to the finish line, including pretty-plotting, additional analyses, and writing. If you are looking for a short, impactful project that will drive your career to the next level, please give us a shot :) 2/n t.co/BENTN756GZ

t.co

https://osu.wd1.myworkdayjobs.com/en-US/OSUCareers/job/Post-Doctoral-Scholar_R103545-1

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Shujun Ou @sigmafacto.bsky.social · 10/04/2025

Hello bluesky world! Newbee here! I have a postdoc position immediately available in my lab. It will focus on identifying high-quality transposons in many genomes and finding their impacts in evolution and traits. Most works, including EDTA2 development and annotation of 400+ genomes, are done! 1/n

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